The RPE is a monolayer of pigmented cells located in the back of the eye between the neural retina and the choroidal blood supply and is critical for normal photoreceptor function. We previously developed and physiologically characterized a human fetal RPE primary culture. The purpose of this project was to examine the expression profiles of RPE cells grown on Primaria flask and human extracellular matrix coated transwells. Total RNA was extracted from four to eight week-old primary cultures of human fetal RPE and reverse transcribed. The biotinylated cRNA was hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array containing 38,500 genes. The normalized gene expression levels were compared between cells grown on flask and transwell. Real-time RT-PCR was used to corroborate some of the differentially expressed genes. RPE cells grown on transwells have approximately 80 genes with lower expression levels and approximately 75 genes with higher expression level compared to cells grown on Primaria flasks. Genes with lower expression levels include K- dependent, Na calcium exchangers, sodium bicarbonate cotransporters, K channels. Genes with higher expression levels include collagens, metallothioneins, decorins. Further comparison to native tissue will help determine which of these culture conditions is more physiologically relevant.